BHARATHIAR UNIVERSITY COIMBATORE – 641 046syllabus.b-u.ac.in/unidepts/1112/biotech1112.pdf · BHARATHIAR UNIVERSITY :: COIMBATORE – 641 046 ... Origin and evolution of microorganisms

M.Sc. Biotech (Univ Dept) 2011-12 Annexure No. 77 A

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BHARATHIAR UNIVERSITY :: COIMBATORE – 641 046

M.Sc. BIOTECHNOLOGY (UNIVERSITY DEPT.)

(For the students admitted during the academic year 2011– 2012 batch & onwards)

SCHEME OF EXAMINATION

Semester Paper Subject

Hrs

/ w

eek

University

examination

To

tal

Mar

ks

Cre

dit

s

Dur/

Hrs

.

INT

.

EX

T

SEMESTER I

11BIOBC01 Paper-I Biochemistry 4 3 25 75 100 4

11BIOBC02 Paper - II Cell and Molecular Biology 4 3 25 75 100 4

11BIOBC03 Paper - III Microbiology 4 3 25 75 100 4

11BIOGE01 Elective 1 Genetics 4 3 25 75 100 4

Supportive1 2 2 12 38 50 2

11BIOBCP1 Practical - I Basic Biotechnology 6 6 25 75 100 4

SEMESTER II

11BIOBC04 Paper – IV Developmental Biology and

Physiology

4 3 25 75 100 4

11BIOBC05 Paper – V Recombinant DNA technology 4 3 25 75 100 4

11BIOBC06 Paper – VI Immunology 4 3 25 75 100 4

11BIOGE02 Elective Bioprocess Technology 4 3 25 75 100 4

Supportive2 2 2 12 38 50 2

11BIOBCP2 Practical –II Advanced Biotechnology 6 6 25 75 100 4

SEMESTER III

11BIOBC07 Paper VII Animal Biotechnology 4 3 25 75 100 4

11BIOBC08 Paper VIII Plant Biotechnology 4 3 25 75 100 4

11BIOBC09 Paper IX Environmental Biotechnology 4 3 25 75 100 4

11BIOGE03 Elective 3 Stem Cell Biology and Tissue

Engineering

4 3 25 75 100 4

Supportive3 2 2 12 38 50 2

11BIOBCP3 Practical III Applied Biotechnology 6 6 25 75 100 4

SEMESTER IV

11BIOBC10 Paper - X Computational Biology 4 3 25 75 100 4

11BIOBC11 Paper - XI Biosafety Bioethics & IPR 4 3 25 75 100 4

11BIOBC12 Paper - XII System Biology 4 3 25 75 100 4

11BIOBC13 Paper - XIII Pharmaceutical Biotechnology 4 3 25 75 100 4

Project Work* - - - 200 8

Total 2250 90

* The report is the bonafied work carried out by the candidate under the guidance of a faculty

authenticated and countersigned by the HOD. This project work must be presented and

defended by the candidate in the department attended by all faculties and reviewed by

external examiner. Candidate who has presented the work as ‘Not qualified as per CBCS’

must resubmit the project again in the ensuing academic year.


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Subject Title : Biochemistry

Course Number : 11BIOBC01 Number of Credits: 4 (Four)

Subject Description :

Preamble:

Scope: This paper presents the study of identification and quantitative determination of the

substances, studies of their structure, determining how they are synthesized metabolized and

degraded in organisms, and elucidating their role in the operation of the organism.

Objective: On the successful completion of the course the students will get an overall

understanding of structure of atoms, molecules and chemical bonds, enzyme kinetics, bio

polymers and metabolic reactions in a living system.

Goal: This paper in biochemistry has been designed to provide the student with a firm

foundation in the biochemical aspects of cellular functions which forms a base for their future

research.

UNIT I

Structure of atoms, molecules and chemical bonds; Classes of organic compounds and

functional groups. Covalent and Noncovalent interactions - Van der Waals, Electrostatic,

Hydrogen bonding and hydrophobic interactions; Respiration and photosynthesis. Chemical

foundations of Biology- pH, pK, acids, bases and buffers, Henderson – Hasselbach equation,

biological buffer solutions.

Energy metabolism (concept of free energy); Principles of thermodynamics; Kinetics,

dissociation and association constants; energy rich bonds; weak interactions; coupled reactions

and oxidative phosphorylation; group transfer; biological energy transducers; bioenergetics.

UNIT II

Sugars - classification and reactions. Polysaccharides: classification, occurrence,

isolation, purification, properties and biological reactions. Structural features of homoglycans,

heteroglycans and complex carbohydrates. Methods for compositional analysis.

Proteins: Amino acids and peptides-classification, chemical reactions and physical

properties. Peptide bond, Primary structure of proteins, structural comparison at secondary and

tertiary levels (Ramchandran map), conformation of proteins and polypeptides (secondary,

tertiary, quaternary and domain structure), Purification and criteria of homogeneity: protein

folding-biophysical and cellular aspects.

Lipids: Classification, structure and functions. Triglycerides; Phospholipids; Steroids and

terpenes. Glyco and lipoproteins - structure and function. Role of lipids in biomembranes.

Nucleic acids: Structure of double stranded DNA (B, A, C, D, T and Z DNA). The

biological significance of double strandedness, sequence dependent variation in the shape of

DNA. Physical properties of double stranded DNA, types of RNAs and their biological


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significance. DNA bending, DNA supercoiling. Conformational properties of polynucleotides,

secondary and tertiary structural features and their analysis.

UNIT III

Enzyme kinetics (negative and positive cooperativity); Regulation of enzymatic activity;

Enzyme catalysis in solution, kinetics and thermodynamic analysis, effects of organic solvents

on enzyme catalysis and structural consequences. Active sites; Enzymes and coenzymes:

Coenzymes interactions: activators and inhibitors, kinetics of enzyme inhibitors, isoenzymes,

allosteric enzymes; Ribozyme, hammer head, hair pin and other ribozymes, strategies for

designing ribozymes. Abzyme: structure and drug targets (enzymes and receptors); Drug

development; Prodrug delivery using enzymes; Bioluminescence

UNITIV

Silk fibroin, coiled coils, collagen triple helix and hemoglobin. Denaturation and

renaturation of proteins. Lysozyme- structure, enzymic activity, mechanism of lysozyme action.

Analytical techniques: separation techniques, small and macro biomolecules, Protein-

Protein and protein-ligand interactions. Physical and chemical methods for immobilization of

small and macro molecules.

UNIT V

Glycolysis and TCA cycle; Glycogen breakdown and synthesis; Gluconeogenesis;

interconversion of hexoses and pentoses: Co-ordinated control of metabolism; Biosynthesis of

purines and pyrimidines; Oxidation of fatty acids; Biosynthesis of fatty acids; Triglycerides;

Phospholipids; Sterols.

References:

1. Biochemistry (3rd

Edition) - Christopher K. Mathews, Kensal E. van Holde, Kevin G.

Ahern, Pearson Education.

2. Principles of Biochemistry – Smith et al., McGraw – Hill International book Company,

8th

Edition.

3. Principles of Biochemistry – Lehninger , Nelson, Cox, CBS publishers

4. Fundamentals of Biochemistry – Voet et al., John Wiley and Sons, Inc.

5. Biochemistry – Zubay , WCB publishers

6. Harper’s Biochemistry – R.K.Murray, D.K.Granner, P.A.Mayes and V.W Rodwell,

Prentice-Hall International.

7. Biochemistry (VIth

Ed.) – J.M Berg; J.L.Tymoczko and L.Stryer, W H Freeman and

Company, NY.


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Subject Title : Cell and Molecular Biology



Scope: This paper provides a thorough knowledge about structure and function of cells, cellular

energetics, protein trafficking, bio molecules and cellular development.

Objective: Understanding the structural and functional aspects of the cell provides the student

with a strong foundation in the molecular mechanisms underlying cellular function.

Goal: Students after completion of this paper will be exceptionally well prepared to pursue

careers in cellular and sub cellular biological research, biomedical research, or medicine or allied

health fields.

UNIT I

Structure and function of cells in prokaryotes and eukaryotes; Structure and organization

of Membrane - Model membranes, Glyco conjugates and proteins in membrane systems;

Response to stress - active and passive, transport channels and pumps, Neurotransmission,

neuromuscular junction. Extra cellular matrix – cell to cell and cell matrix adhesion – selectins,

integrins, cadherins, gap junctions.

UNIT II Mitochondria – structure, biogenesis; Chloroplast – structure, biogenesis; Molecular

events of electron transport chain, ATP synthesis, photosynthesis and photorespiration. Structure

of Endoplasmic reticulum, Golgi complex, lysosomes; protein synthesis and post translational

modification; of proteins vesicular transport and import into cell organelles

UNIT III

Oxidative reactions in microbodies and nucleus. The nucleosome, the supranucleosomal

structures. Nucleic acid structure: DNA and RNA; DNA replication; transcription and

translation. Gene regulation: prokaryotic gene regulation- Operon concept; lac operon and

tryptophan operon; Eukaryotic gene regulation: transcriptional and translational regulations.

UNIT IV

Mechanism of cell division: regulation of cell cycle; factors and genes regulating cell

cycle. Cell signaling – types of cell signaling - G protein mediated, Tyrosine kinase mediated

signaling. Biochemistry and molecular biology of Cancer, tumor suppressor and oncogenes.

UNIT V

Cellular signaling; cell differentiation; gametogenesis and fertilization; life cycle and

molecular biology of some pathogens – AIDS virus, tuberculosis, malarial parasite, hepatitis

virus, filarial parasite and kalazar parasite


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Techniques (Self Study):

Radiolabelling techniques: Properties of different types of radioisotopes normally used in

biology, their detection and measurement; incorporation of radioisotopes in biological tissues

and cells, molecular imaging of radioactive material, safety guidelines.

References

1. Molecular cell Biology, by Darnell, Lodish, Baltimore, Scientific American Books, Inc.,

1994.

2. Molecular and cellular Biology, Stephen L.Wolfe, Wadsworth Publishing Company, 1993.

3. Molecular Cloning: a Laboratory Manual, J. Sambrook, E.F. Fritsch and T. Maniatis, Cold

Spring Harbor Laboratory Press, New York, 2000.

4. Introduction to Practical Molecular Biology, P.D.Dabre, John Wiley & Sons Ltd., New York,

1998.

5. Molecular Biology LabFax, T.A. Brown (Ed.), Bios Scientific Publishers Ltd., Oxfor, 1991.

6. Molecular Biology of the Gene (4th

Edition), J.D.Watson, N.H.Hopkins, J.W.Roberts, J.A.

Steitz and A.M.Weiner, The Benjamin/Cummings Publ. Co., Inc., California, 1987.

7. Genes VI (6th

Edition ) Benjamin Lewin, Oxford University Press, U.K., 1998

Subject Title : Microbiology



Scope: This paper provides the knowledge about different types of microorganisms and their

identification techniques in modern biology and there by the usefulness of the techniques in

research and commercial purposes.

Objectives: In order to make the students to understand the identification of microorganism

based on the advanced microbiological methods and applications of microorganisms.

Goal: Students can gain the idea of how to identify the microorganisms based on the modern

microbiological approach.

UNIT – I

Microbial Bio-diversity: Origin and evolution of microorganisms – concepts of species

and hierarchical taxa, Bergy’s system of classification: Bacteria, Fungi, Viruses; Biological

nomenclature - Measurement of species richness and evenness: Simpson's diversity index –

Multivariate analysis. Preservation and maintenance of microbes - Microbial Culture Collection

centers – India and International organizations.

UNIT – II

Molecular Taxonomy: Molecular systematics: Polyphasic approach –16S rRNA gene

sequencing, Phylogenetic grouping. Mol % G+C analysis, DNA-DNA hybridization, Fatty Acid

Methyl Ester (FAME) analysis, peptidoglycan, Isoprenoid and quinines. Microbial Community

analysis: DGGE, TGGE, SSCP, T-RFLP, FISH.


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UNIT – III

Soil Microbiology: Soil Environment – Microbial Phylogeny and Diversity in Soil –

Bacteria, Archae, Protozoa, Fungi and other Protista. Microorganisms Cycling Soil Nutrients and

their Diversity. Microbial Interactions in Soil; Horizontal Gene Transfer and Microevolution in

Soil. Soil Microbial Communities and Global climate change. Plant Associated Bacteria – Life

Style and Molecular Interactions; Plant growth promoting bacteria; Biological pesticides for

control of seed and soil borne plant pathogens. Biosensors to monitor Soil Health – soil

suppressiveness to plant diseases – Biodegradation and bioremediation of organic pollutants in

soil – Statistical analyses of microbiological and Environmental data.

UNIT – IV

Medical Microbiology: Bacterial Diseases: Host parasite relationship, epidemiology, pathogenesis, prevention

and treatment - Gram positive cocci; Staphylococcus and Micrococcus; Streptococcus;

Enterococcus. Gram positive rods – Coryneforms, Listeria, Mycobacterium and Nocardia. Gram

negative rods - Klebseilla, Salmonella, Shigella, Neisseria, Haemophilus and Pseudomonas and

Anaerobic bacteria - Clostridium.

Viral Diseases: Classification of virus, epidemiology, pathogenesis, prevention and

treatment - Small pox, common cold, Influenza, Measles, Mumps, Rubella, Arbovirus infections,

Polio, Rabies, Hepatitis, AIDS, Herpes virus infections.

Fungal Diseases: Superficial mycosis, subcutaneous mycosis and systemic mycosis.

Protozoan Diseases: Protozoan infections, Nematode infections, and Trematode

infections. Mycoplasma and other infections: Mycoplasma - Zoonotic and Nosocomial

infections. Diagnosis of infectious diseases; Immunoassays, molecular detection and

identification using variants of PCR.

UNIT –V

Metagenomics - culture independent studies: Exploring and exploiting the microbial

Gene pool. Methods to detect and quantify bacteria in various ecological niches – Analysis of

microbial communities in microhabitats using FISH – Functional characterization of microbial

communities by mRNA analysis – Detection of active bacterial populations in soil.

REFERECES:

1. Microbiology by Lansing M. Prescott

2. Microbial Diversity - Form and Function in Prokaryotes By Oladele Ogunseitan

3. Molecular Microbial Ecology by Dr. A. Mark Osborn and Dr. Cindy J. Smith. Taylor and

Francis Group.

4. Modern Soil Microbiology, Janet Dirk Van Elsas, Janet K. Jansson, Jack T. Trevors –

CRC Press – ISBN 0-8247-2749-5.

5. Greenwood D (2007). Medical Microbiology. I.K. International.

6. Medical Microbiology, Vol. 1: Microbial Infection, Vol. 2: Practical Medical

Microbiology, - Mackie and McCartney.

7. Diagnostic Microbiology, Authors- Baron, Peterson and Finegold.

8. Medical Microbiology by S. Rajan, MJP Publishers

9. Molecular identification, systematics, and population structure of prokaryotes By Erko

Stackebrandt


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Subject Title: Genetics (Elective –I)

Course Number: 11BIOGE01 Number of Credits: 4 (Four)

Subject Description:

Scope: This paper in genetics has been structured to give the student an in depth knowledge of

the organization of the genome in prokaryotes and eukaryotes, the principles of genetic

inheritance and other vital aspects such as Hardy Weinberg law, pedigree analysis and the

genetic basis of disease inheritance.

Objective: The major objective of the paper is to envisage thorough knowledge in genetics and

genome organizations in organisms.

Goal: After successful completion of the paper the students will get an overall view about

genetic makeup of organisms and can take up a career in research.

UNIT I

Genome Organization in prokaryotes: genome of bacteria, bacteriophage and viruses,

plasmids. The fine structure of a prokaryote gene; Genetics of bacteria: transformation,

conjugation, transduction; the genetic map of E.coli genetic recombination. Genetics of viruses:

Life cycle of virulent bacteriophages, temperate phages and prophage; genetic recombination in

phages; mapping genes in phage lambda; The RNA phages, tumor viruses and cancer; viroids.

UNIT II

Genome Organization in Eukaryotes, variation in chromosome number: haploidy,

polyploidy, aneuploidy. Variation in chromosome structure: deficiency of deletion, duplication,

translocation, inversion and B-chromosome. The fine structure of Eukaryote gene;

complementation test, pseudo alleles, split genes, overlapping genes; transposons. Linkage and

crossing over; The three point cross; double crossing over, cytological basis of crossing over; sex

linkage; recombination in neurospora.

UNIT III

Principles of Mendelian inheritance; Mendel’s experiments-monohybrid, dihybrid,

trihybrid and multihybrid crosses. Interaction of genes: incomplete dominance, codominance,

epistasis, complementary genes, duplicate genes, polymeric genes, modifying genes; Pleotrophy,

genome imprinting, inheritance and lethal genes. Environment and gene expression: penetrance

and expressivity; temperature, light, phenocopies. Quantitative or polygenic inheritance:

Inheritance of kernel color in wheat; corolla length in tobacco skin color inheritance in man,

transgressive and regressive variation. Multiple alleles; Sex determination; extra chromosomal

inheritance.

UNIT IV

Human Genetics: Introduction to Human Genetics. Human Chromosomes: Structure and

organization of DNA; Normal human karyotype: Paris Nomenclature; Chromosomal aberration:

Numerical: Aneuploidy, Polyploidy (eg: Turner, Down & Klinefelter Syndromes). Structural:

Translocation, Duplication, Inversion, Ring Chromosome and Deletion (Eg: Cri-du-chat

syndrome). Others: Mosaic, Chimera [Individual with two cell lines] Mendelian Traits: Straight


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hair, Curly hair, Blue and Brown colour of the eyes, Rolling of the tongue, attached and free ear

lobes and Hypertrichosis.

UNIT V

Clinical genetics: Genetic Diseases and Inheritance Pattern: Autosomal inheritance –

Dominant (Eg: Adult polycystic kidney, Achondroplasia & eurofibromatosis.); Autosomal

inheritance – Recessive (Eg: Albinism, Sickle Cell Anemia, Phenyl Ketonuria); X-linked :

Recessive (Eg: Duchenne muscular dystrophy – DMD); X-linked : Dominant (eg. Xg blood

group); Y-linked inheritance (Holandric – eg. Testes determining factor); Multifactorial

inheritance (Eg: Congenital malformations – Cleft lip & palate, Rheumatoid arthritis and

Diabetes. Pedigree studies: Symbols used in pedigree analysis. Pedigree analysis of important

genetic diseases like Haemophilia, Color blindness, Duchenne Musculat Dystrophy (DMD).

How normal genes work; Mechanism of disease. Diagnosis of disease: cytogenetics; Molecular

cytogenetics, molelcular genetics ; cancer genetics. Prevention of disease: Prenatal diagnosis;

Genetic counseling.

References

1. The science of Genetics by Alan G. Atherly, Jack. R, Girton, Jhon. F, Mc Donald.

Sounders college publishers.

2. Genes VII by Benjamin Lewin

3. Hartl. D.L. A primer of population genetics. III edition, Sinauer associates inc.

Sunderland, 2000

4. Molecular cell Biology, Darnell, Lodish, Baltimore, Scientific American Books, Inc.,

1994.

5. Molecular and cellular Biology, Stephen L.Wolfe, Wadsworth Publishing

Company, 1993.

6. Human genetics, A.Gardner, R.T.Howell and T.Davies, Published by Vinod Vasishtha

for Viva Books private limited, 2008. Publishe


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Subject title : Developmental Biology and Physiology

Course number : 11BIOBCB04 Number of credits: 4 (Four)

Scope:

This paper encodes information on the physiology of various eukaryotic systems.

Objective:

To enable the students to know the actual path of physiological metabolism of different living

system.

Goal:

The information gained will help the students to understand the various living system which will

help in the future to develop the drugs.

.

Unit I:

Basic concepts of development:

Production of gametes, cell surface molecules in sperm egg recognition in animals;

zygote formation, cleavage, blastula formation, embryonic fields, gastrulation and formation of

germ layers in animals; Morphogenesis and organogenesis in animals (Drosophila, Amphibia

and Chick). Potency, commitment, specification, induction, competence, determination and

differentiation; morphogenetic gradients; cell fate and cell lineages; genomic equivalence and the

cytoplasmic determinants; imprinting. Embryogenesis in plants (Arabidopsis).

Unit II:

Plant system physiology:

Photosynthesis: Mechanism of photosynthesis; Plant hormones: biosynthesis, storage,

breakdown and transport; physiological effects and mechanism of action. Structure, function and

mechanisms of action of phytochromes, cryptochromes and phototropins; stomatal movement;

photoperiodism. Uptake, transport and translocation of water, ions, solutes and macromolecules

from soil, through cells, across membranes, through xylem and phloem; transpiration;

mechanisms of loading and unloading of photoassimilates, biosynthesis of terpenes, phenols and

nitrogenous compounds and their roles. Responses of plants to biotic (pathogen and insects) and

abiotic (water, temperature and salt) stresses; mechanisms of resistance to biotic stress and

tolerance to abiotic stress.

Unit III

Animal system physiology: Digestion and Haematology:

Homeostasis, nutrition, structure and functions of digestive system. Physiology of

digestion. Blood corpuscules, haemopoiesis, plasma function, blood volume, haemostasis.

Comparative anatomy of heart structure, myogenic heart, ECG- its principle and significance,

cardiac cycle, heart as a pump, blood pressure, neural and chemical regulation of all above.

Unit IV

Respiration and Excretion: Comparison of respiration in different species, anatomical considerations, transport of

gases, exchange of gases, waste elimination, neural and chemical regulation of respiration.


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Comparative physiology of excretion, kidney, urine formation, urine concentration, waste

elimination, micturition, regulation of water balance, electrolyte balance and acid-base balance.

Unit V:

Nervous system:

Neurons, action potential, gross neuroanatomy of the brain and spinal cord, central and

peripheral nervous system. Types, structure and functions of muscles, Physiology of musle

contraction. Sense organs: vision, hearing and tactile response. Endocrine glands, basic

mechanism of hormone action, hormone and diseases; reproductive processes, neuroendocrine

regulation. Thermoregulation.

Reference:

1. An introduction to embryology- Balinsky

2. Developmental biology- Gilbert

3. Chordate embryology- Verma, Agarwal and Tyagi

4. Plant physiology by Delwin and Withem

5. Plant physiology by Lincoin Taiz, Eduardo Zeiger Publishers, Sinauer

Subject Title : Recombinant DNA technology



Scope: This paper provides the student a thorough knowledge in principles and methods in

genetic engineering, vectors in gene cloning, transformation in higher organisms, Human

Genome Project and gene therapy. Techniques employed are carved as self study.

Objective: The main objective of the paper is to expose students to application of rDNA

technology to various fields of biotechnology.( medicine and research areas).

Goal: This paper will help the student to get a grasp on the latest advances in recombinant DNA

technology, which is a powerful tool in modern Biotechnology

UNIT- I

Principles and methods in genetic engineering: Isolation and purification of Nucleic

Acids - Agarose Gel Electrophoresis - Southern, Northern and South-Western blotting

techniques - Principles and techniques of nucleic acid hybridization and cot curves - Polymerase

Chain Reaction: Methods and advancements.

Enzymes in Molcular Biology: Nucleases, Restriction endonucleases, DNA Ligases,

topoisomerases, gyrases, methylases, other modifying enzymes – Bacterial Transformation:

Principles and methods.

UNIT-II

Vectors in Gene Cloning: Plasmids, Bacteriophages, Phagemids, Cosmids - Artificial

Chromosomes: PAC, BAC, YAC. Cloning in Prokaryotes (E.coli). Cloning in Organisms other

than E.coli: (Pseudomonas, Bacillus subtilis, Yeast and Fungi). cDNA sysnthesize and

cloning:mRNA enrichment, Reverse transcription,DNA primers,Linkers,Adaptors. Library


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construction and screening: Alternative strategies for gene cloning:cloning interaction genes.

Two and three hybrid systems - Gene expression in Prokaryotes: merits and demerits –

examples. How to study gene regulation? DNA transactions, primer extension, S1 Mapping,

Rnase protection assay, Reporter assay.

UNIT-III

Expression strategies for heterologous genes.: vector engineering and codon

optimization, host engineering, in vitro transcription and translation, expression in bacteria ,

yeast, insect, insect cells, mammalian cells, phage display.

UNIT-IV

A. Mapping of genome: Genetic and physical maps, physical mapping and map based

cloning, choice of mapping population, simple sequence repeat loci, southern and

fluorescence in situ hybridization for genome anlalysis, chromosome micro decection and

micro cloning ,molecular markers in genome analysis; RFLP, RAPD and AFLP analysis,

molecular markers linked to disease resistance genes ,application of RFLP in forensic,

disease prognosis, genetic counseling.

B. Genome sequencing: Genomic libraries, YAC, BAC libraries, strategies for genome,

packaging, transaction and recovery of clones, application of sequence information for

defective gene identification.

UNIT-V

Gene Therapy: Strategies for gene delivery gene replacement/augmentation, gene

correction, gene editing, gene regulation and silencing,Si/micro RNA, antisense RNA, non

coding RNAs regulation of genes. Gene therapy for inherited diseases, ADA, FH, Cystic

Fibrosis, DMA, Neoplastic disorders, infectious diseases. Somatic Cell Gene therapy, Triple

helix therapeutics, Antisense oligonucleotides, Ribozymes, Aptamers.DNA vaccines,

Applications in medicine.Transgenic and gene knockout technologies: targeted gene

replacement, chromosome engineering.


Molecular biology and recombinant DNA methods: Isolation and purification of RNA ,

DNA (genomic and plasmid) and proteins, different separation methods; analysis of RNA, DNA

and proteins by one and two dimensional gel electrophoresis, isoelectric focusing gels; molecular

cloning of DNA or RNA fragments in bacterial and eukaryotic systems; expression of

recombinant proteins using bacterial, animal and plant vectors; isolation of specific nucleic acid

sequences; generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC and YAC

vectors; in vitro mutagenesis and deletion techniques, Epigenetic inheritance, gene knock out in

bacterial and eukaryotic organisms; protein sequencing methods, detection of post-translation

modification of proteins; DNA sequencing methods, strategies for genome sequencing; methods

for analysis of gene expression at RNA and protein level, large scale expression analysis, such as

micro array based techniques; isolation, separation and analysis of carbohydrate and lipid

molecules; RFLP, RAPD and AFLP techniques.


Page 12 of 33 SCAA Dt. 23.03.2011

References:

1. Primrose. S.B., Twyman R.M., Old. R.W. (2001) Pricinciples of Gene Manipulation.

Blackwell Science Limited.

2. Molecular and cellular methods in Biology and Medicine, P.B. Kaufman, W.Wu, D.Kim

and L.J: Cseke, CRC Press, Florida, 1995.

3. Molecular Biotechnology: Principles and Applications of Recombinant DNA.

4. Bernard R. Glick,Jack J. Pasternak, Asm Press.

5. Methods in Enzymology Vol.152, guide to molecular cloning Techniques, S.L. Berger

and A.R.Kimmel, Academic Press, Inc. San Diego, 1998

6. Methods in Enzymology Vol 185, Gene Expression Technology, D.V. Goeddel,

Academic Press, Inc., San Diego, 1990

7. DNA Science, A First Course in Recombinant Technology, D.A.Mickloss and

G.A.Freyar, Cold Spring Harbor Laboratory Press, New York, 1990.

8. Molecular Biotechnology (2nd

Edition), S.B.Primrose, Blackwell Scientific Publishers,

Oxford, 1994.

9. Milestones in Biotechnology. Classic papers on Genetic Engineering, J.A. Davies and

W.S. Reznikoff, Butterworth-Heinemann, Boston, 1992.

10. Route Maps in Gene Technology, M.R.Walker and R.Rapley, Blackwell Science Ltd.,

Oxford, 1997.

11. Genetic Engineering. An introduction to gene analysis and exploitation in Eukaryotes,

S.M. Kingsman and A.J. Kingsman, Blackwell Scientific Publications, Oxford, 1998

12. Human Molecular Genetics, Tom Strachan and Andrew P.Read, Bios Scientific

Publishers, 1996.

13. LEWIN’S Gene X, J E. Krebs, E.S. Goldstein and S.T. Kilpatrick, Jones and bartlett

Publishers, London.

Subject Title : Immunology



Scope: Understanding the immune system, antigen antibody reactions, applications of

immunological techniques, humoral and cell mediated immunity, hypersensitivity reactions and

hybridoma technology.

Objective: To expose the students with various immune systems of human body.

Goal: This course will provide the student insights into the various aspects of Immunology such

as classical immunology, clinical immunology, Immunotherapy and diagnostic immunology.

UNIT I

The Immune System: Innate Immune response and its role in protection. Adaptive

Immune response, the humoral and cellular component of the Immune response, Overlap


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between Innate and adaptive immunity. Cells involved in the Immune response: Macrophages,

B and T lymphocytes, Dendritic cells, Natural killer and Lymphokine activated killer cells,

Eosinophils, Neutrophils and Mast cells. The lymphoid organs: Bone marrow, Spleen, lymph

nodes, MALT. Haemopoiesis and differentiation, lymphocyte trafficking.

UNIT II

The antigens seen by the Immune System: Antigenicity and Immunogenicity. The

epitopes seen by B Cells and T Cells. Antibody Molecule: Structure of antibody molecules;

Function of antibody molecules; Antibody-Antigen interactions; Immunization protocol; The

various immunotechniques for detection and quantification of antigens/antibodies: RID, ODD,

immunoelectrophoresis, rocket immunoelectrophoresis, RIA, ELISA, western blot,

floweytometry and immunofluorescence microscopy including in situ localization techniques

such as FISH and GISH. Generation of antibody diversity. Antibody engineering: Hybridoma

secreting monoclonal antibodies-Recombinant antibody molecules. Catalytic Antibodies.

UNIT III

Major Histocompatibility Complex: MHC molecules and organization of their genes;

Structure and function of MHC gene products. Antigen Presentation: Antigen processing; Role

of MHC and non-MHC molecules in antigen presentation. Structure of TCR and its interaction

With MHC-I and MHC-II peptide Complex - T cell selection. Organization of TCR gene

segments and their rearrangement. Activation of T-cells; Activation TH and TC cells; Generation

of T memory cells; Apoptosis in T cells. B-Cell maturation: Activation of B Cells; Regulation of

B-Cell mediated effector functions.

UNIT IV

Cytokines: structure of Cytokines; function of Cytokines. The Complement System. Cell

mediated effector responses. Immune suppression and immune tolerance. Transplantation

immunology- MLR, HLA Typing, Bone marrow transplantation, Organ transplants.

UNIT V

Hypersensitivity reactions, Autoimmune disorders, Immunity to Infectious agents -

Bacteria, Viruses, Malaria, Anthrax and Helminthes. Tumor immunology, Tumor antigens,

immune response to tumors, cancer immunotherapy Vaccine technology and recombinant

vaccines.

References

1. J.Kuby, 2003, Immunology 5th

edition, W.H. Freeman and Company, Newyork..

2. C.V.Rao. 2002, An Introduction to Immunology, Narosa Publishing House, Chennai.

3. K.M.Pavri. 1996, Challenge of AIDS, National Book Trust, India.

4. I.R.Tizard, 1995, Immunology: An Introduction , 4th edition , Saunders College Publishers,

New York.

5. I.Roitt, 1994, Essential Immunology, Blackwell Science, Singapore.

6. A. Bul and K.Abbas, 1994, Cellular and Molecular immunology


Page 14 of 33 SCAA Dt. 23.03.2011

Subject Title : Bioprocess Technology (Elective –II)

Course Number : 11BIOGE02 Number of Credits: 4 (Four)


Core course : Bioprocess engineering / Bioprocess technology

Scope: This paper provides the thorough knowledge about types of microorganisms and their

applications and there by producing various products of industrial and commercial uses.

Objective: In order make the students to understand the applications and uses of

microorganisms.

Goal: Students will get the idea of fermentation technology and to produce economically

important products and help to find out new methods and applications of microorganisms.

Unit I

Fundamentals of Bioprocess engineering: Introduction to bioprocess engineering.

Media design and usage in fermentation: Types of media, composition of media – carbon

sources, nitrogen sources, vitamins and growth factors, mineral, inducers, precursors and

inhibitors.

Microbial Growth: Isolation, Preservation and Maintenance of Industrial

Microorganisms.

Inoculum development: Development of inocula for yeast, bacterial, mycelial and

vegetative fungal processes; aseptic inoculation of the fermentor.

Proteins as enzymes, Immobilized enzymes: methods, Industrial enzymes.

UNIT- II

Sterilization methods: Moist heat; dry heat, flame, filter, gas (ethylene oxide), HTST

(high temperature/short time) treatments – continuous sterilizers and pasteurizers - Sterility,

asepsis– medium sterilization, batch sterilization, contiuous sterilization, filter sterilization.

Microbial growth kinetics: Factors affecting microbial growth. Fermentation kinetics:

Quantitative description of cellular process, Mass balances for bioreactors, Kinetic modeling,

Population models.

Production Kinetics: Design for single and multiple reactions - size comparisons of

single reactor for single reactions, multiple reactor systems for single reaction, reactions in

parallel, in series, and series-parallel reactions of first order. Heterogeneous reactions, kinetics

and mechanism of heterogeneous, non catalytic, and catalytic reactions.

UNIT –III

Bioreactors: Introduction to bioreactors; Batch and Fed-batch bioreactors, Continuous

bioreactors; solid state and submerged; aerobic and anaerobic fermentation; mixed microbial

populations; immobilization of cells and co-immobilization; immobilized cell reactors;

Bioreactor operation; Sterilization; Aeration; Sensors; Instrumentation; Analysis of mixed

microbial populations, specialized bioreactors (pulsed, fluidized, photobioreactors etc.,).


Page 15 of 33 SCAA Dt. 23.03.2011

Design of Bioreactors:Construction material; Basic components – Agitator, aerator,

Valves and steam traps,seals, stirrer glands; measurement and control of parameters (online and

off line sensors) – temperature, flow rate, pressure, pH, DO, gas analysis, control pathways,

computer in controlling; Air-lift, stirred tank, tower, fluidized bed, packed bed, pulsed, photo

bioreactors.

UNIT -IV

Downstream Processing: Biomass removal: separation of microbial cells and solid

matter; Centrifugation; Sedimentation; Flocculation; Microfiltration; Disintegration of

microorganism: Sonication; Bead mills; Homogenizers; Chemical lysis; Enzymatic lysis;

Membrane based purification: Ultrafiltration ; Reverse osmosis; Dialysis ; Diafiltration ;

Adsorption and chromatography: size, charge, shape, hydrophobic interactions, Biological

affinity; Process configurations (packed bed, expanded bed, simulated moving beds);

Precipitation (Ammonium Sulfate, solvent); Electrophoresis(capillary); Extraction(solvent,

aqueous two phase, super critical), Drying – spray driers, drum driers and freeze driers.

UNIT –V

Microbial products in pharmaceutical, food and agriculture industry: Production,

harvest, recovery and uses – enzymes, Antibiotics (penicillins, tetracycline, streptomycin),

vitamins (B2, B12), Aminoacids (lysine, glutamic acid, arginine, threonine), Organic solvents

(acetone, butanol, ethanol, glycerol); Organic acids (acetic acid, citric acid, lactic acid). Use of

microbes in mineral beneficiation and oil recovery.

Production, harvest, recovery and uses – Baker’s yeast, milk products, edible mushrooms. Single

Cell Protein (algae/fungi).

Biofertilizer (Rhizobium, Azospirillum, Azolla, Phosphobacteria), Biopesticides

(Bacillus thruingiensis, NPV, Pseudomonas)

Reference:

1. Principles of fermentation technology by P.F. Stanbury and A.Whitaker, Pergamon press.

Second edition. 2005.

2. Fermentation microbiology and Biotechnology. Second edition, edited by El-.Mansi,

C.F.A. Bryce, A.L. Demain, A.R. Allman. Taylor and Francis, 2007.

3. Introduction to Biochemical engineering by D.G.Rao, McGraw-Hill publications, I

edition, 2007.

4. Industrial Microbiology by Prescott and Dunns 4th

edition edited by Gerald Reed,

Chapman & Hall publications 2007.

5. Industrial microbiology by L. E. Cassida Jr.


Page 16 of 33 SCAA Dt. 23.03.2011

Subject Title : Animal Biotechnology



Scope: The study of animal cells has helped us gain an insight not only in the structure and

function of cells and tissues but also in different physiological, biochemical and immunological

processes. Biotechnologists explore and develop new technologies using molecular biology,

embryo manipulation and cell and tissue culture. Research on gene regulation and early embryo

development has resulted in novel techniques to manipulate and explore the genomes of

domestic animals for ways to increase healthier food production as well as to develop biomedical

applications.

Objective: The major objective is to provide a world-class training experience for these students

in an interdisciplinary research program connecting animal genomics with animal reproduction

and biotechnology.

Goal: This paper will help students interested in careers as laboratory, research or animal care

technicians in the fields of veterinary and human health or biotechnology.

UNIT I

Introduction to Animal Tissue Culture: Background, Advantages, Limitations, and

applications. Culture Environment, Cell Adhesion, Cell Proliferation and Cell differentiation.

Essential Equipments required for animal tissue culture, Aseptic Technique, Objectives,

Elements, Sterile Handling, Risk Assessment and General Safety. Media: Physicochemical

Properties, Balanced Salt Solutions, Complete Media, Serum, Disadvantages of Serum

supplemented media, Serum-Free Media, Advantages of Serum-Free media.

UNIT II

Primary Culture: Isolation of Tissue, Steps involved in primary cell culture, Cell Lines,

Nomenclature, Subculture and Propagation, Immortalization of cell lines, Cell line designations,

Routine maintenance. Characterization of Cell Line: Need for characterization, Morphology,

Chromosome Analysis, DNA, RNA and Protein Content, Enzyme Activity and Antigenic

Markers. Transformation of animal cell, Immortalization, Aberrant Growth Control,

Tumorogenicity, Cell counting, Cell Proliferation, Plating Efficiency, Labeling Index,

Generation Time of established cell line.

UNIT III

Contamination: Source of contamination, Type of microbial contamination, Monitoring,

Eradication of Contamination, Cross-Contamination. Cryopreservation: Need of

Cryopreservation, Preservation, Cell banks, Transporting Cells. Cytotoxicity: measurement of

cell death; Apoptosis and its determination; Cytotoxicity assays. Application of animal cell

culture ; Vaccine production; Tissue engineering; Engineered cell culture as source of valuable

products and therapeutic protein production.


Page 17 of 33 SCAA Dt. 23.03.2011

UNIT IV

Transgenic Animals: Production Methodology-Embryonic Stem Cell method,

Microinjection method, Retroviral vector method; Applications of transgenic animals-in

therapeutic protein production; live stock improvement; Transgenic animals as disease models.

Gene Therapy: Ex-vivo gene therapy, In vivo gene therapy, Germline gene therapy and Somatic

gene therapy ; Vectors in gene therapy: Viral gene delivery system- Retrovirus vector system,

Adenovirus vector system, Adeno-Associated virus vector system, Herpex simplex virus vector

system; Non-viral gene delivery system; Prodrug activation therapy; Nucleic acid therapeutic

agents. Gene targeting, silencing and knockout technologies.

UNIT V

In Vitro Fertilization and Embryo Transfer: Composition of IVF media, Steps involved in

IVF, Fertilization by means of micro insemination, PZD, ICSI, SUZI, MESA. Stem cell culture,

embryonic stem cell and their applications. Ethical issues in animal biotechnology.

References

1. Animal cell culture; A practical approach, 4th Edition, by Freshney. R.I. John Wiley

publication.

2. Methods in cell biology; Volume 57, Animal cell culture methods, Ed. Jennie

P.Mather, David Barnes, Academic press.

3. Mammalian cell biotechnology; A practical approach, Ed. M. Butler, Oxford

university press.

4. Exploring genetic mechanism; Ed. Maxine Singer and Paul Berg.

5. Principles of genetic manipulation; Ed. Old and Primrose, 6th Edition. Blackwell

science publication.

Subject Title : Plant Biotechnology


Subject Description

Scope: Students will learn about genome organization in plants, basic techniques in tissue

culture and its applications, Genetic transformation in plants, metabolic engineering, production

of pharmaceuticals and industrial products.

Objective: To equip students to fully aware of the applications of plant biotechnology.

Goal: This paper has been designed to give the students comprehensive training in the plant

biotechnology and its application for increasing agricultural production, environment

improvement, human, nutrition and health. Help students to get a career in both industry/R&D.

UNIT – I

Genome organization in Plants: Nucleus, Chloroplast and Mitochondria, Molecular

Marker-aided Breeding: RFLP maps, linkage analysis, RAPD markers, STS, Microsatellites,


Page 18 of 33 SCAA Dt. 23.03.2011

SCAR (Sequence Characterized Amplified Regions), SSCP (Single Strand Conformational

Polymorphism), AFLP, QTL, map based cloning, molecular marker assisted selection.

UNIT – II

Plant Cell and Tissue Culture: Tissue culture media (composition and preparation),

Callus and suspension culture; Somaclonal variation; Micropropagation; Organogenesis; Somatic

embryogenesis; transfer and establishment of whole plants in soil; green house technology.

Embryo culture and embryo rescue. Artificial seeds. Protoplast fusion and somatic hybridization;

cybrids; anther, pollen and ovary culture for production of haploid plants. Cryopreservation and

DNA banking for germplasm conservation.

UNIT – III

Plant Genetic Transformation methods: Features of Ti and Ri plasmids and its use as

vectors, binary vectors, viral vectors, 35S and other promoters, use of reporter genes and marker

genes, Gene transfer methods in plants: direct and indirect DNA transfer. Chloroplast

transformation and its advantages. Transgene stability and gene silencing.

UNIT – IV

Application of Plant Genetic Transformation: Herbicide resistance: phosphoinothricin,

glyphosate, sufonyl urea and atrazine. Insect resistance: Bt genes, non-Bt genes like protease

inhibitors, alpha amylase inhibitor. Disease resistance: chitinase, 1,3-beta glucanase, RIP,

antifungal proteins, thionins, PR proteins; Virus resistance: coat protein mediated, nucleocapsid

gene. Nematode resistance. Abiotic stress: Drought, cold and salt. Post-harvest losses: long shelf

life of fruits and flowers, use of ACC synthase, polygalacturanase, ACC oxidase, male sterile

lines, bar and barnase systems, carbohydrate composition and storage, ADP glucose

pyrophosphatase, RNAi and Reverse genetics.

UNIT – V

Metabolic Engineering and Biopharmaceuticals: Plant secondary metabolites, control

mechanisms and manipulation of phenylproponoid pathway, shikimate pathway; alkaloids,

industrial enzymes, biodegradable plastics, polyhydroxybutyrate, therapeutic proteins, lysosomal

enzymes, antibodies, edible vaccines, purification strategies, oleosin partitioning technology,

Plant host-insect interactions- nif and nod genes.

References

1. An introduction to genetic engineering in plants, Mantel, Mathews and Mickee, 1985.

Blackwell Scientific Publishers. London.

2. In Vitro culture of higher plants by R.L.M. Pierik, 1987. Martinus Nijhoff Publisher,

Dordrecht.

3. Plant cell culture. A practical approach. Second edition. Edited by R.A. Dixon and R.A.

Gonzales.1994.Oxford University Press. Oxford.

4. Plant Molecular Biology by Donald Grierson and S.V. Convey.1984. Blackie and Son

Limited. New York

5. Plant Biotechnology by Mantell, S.H and Smith, H. 1983. Cambridge University press,

UK


Page 19 of 33 SCAA Dt. 23.03.2011

6. Plants, genes and agriculture by M.J. Chrispeels and D.F. Sadava.2000.The American

Scientific Publishers, USA.

7. Practical Application of Plant Molecular Biology by R.J. Henry.1997. Chapmans and

Hall.

8. Plant Biotechnology by J.Hammond, P. Mc Garvey and V. Yusibov 2000

Springer Verlag, UK

9. Plant Biotechnology and Transgenic Plants, Edited by Kirsi-Marja Oksman-

Caldentey and Wolfgang H. Barz. 2002, Marcel Dekker, Inc. New York.

10. Plant Biotechnology (The genetic manipulation of plants) by Adrian Slater, Nigel W.

Scott and Mark R. Fowler, 2003, Oxford University press, UK.

11. Molecular Plant Biology: A practical approach (Vol. I and II), Edited by

Gilmartin and Bowler, 2002, Oxford University press, UK.

Subject Title : Environmental Biotechnology


Subject Description

Scope: To understand the energy sources, environmental pollution and remediation using

biotechnology and its control.

Objective: Students will get an idea about the hazards to our environment, solutions to protect

and for sustainable development.

Goal: This course is important in the era of industrialization leading to environmental hazards

and hence will help students to take up a career in tackling industrial pollution and also who is

willing to take up the research in areas like development of biological systems for remediation of

contaminated environments (land, air, water), and for environment-friendly processes such as

green manufacturing technologies and sustainable development.

UNIT - I

Bio-Fuels and Bio-Energy: Biofuels and sources, Advantages, Genetic improvement

through metabolic engineering; Commercial success of Biofuels, Future energy needs and

direction of research.

UNIT – II

Environmental pollution: Types of pollution, methods for the measurement of

pollution, air pollution and its control, Global environmental problems: ozone depletion, green

house effect and acid rain, principles of conservation and application of biotechnology, remote

sensing and GIS (Principal and applications in ecological mapping and environmental hazard

predictions), ecological modeling, bioindicators and biosensors for detection of pollution. Solid

waste: Sources and management (composting, vermiculture and methane production).


Page 20 of 33 SCAA Dt. 23.03.2011

UNIT – III

Water Pollution and control: Need for water management, measurement and sources,

water pollution. Waste water treatment: waste water collection, physico-chemical properties of

waste water, physical, chemical and biological treatment processes. activated sludge, oxidation

ditches, trickling filter, rotating discs, rotating drums, oxidation ponds. Anaerobic digestion,

anaerobic filters, up flow anaerobic sludge blanket reactors. Treatment schemes for waste waters

of dairy, distillery, tannery, sugar, antibiotic industries.

UNIT – IV

Xenobiotics: Ecological considerations, degradative plasmids; hydrocarbons, substituted

hydrocarbons, oil pollution, surfactants, pesticides. biopesticides; bioremediation and

Phytoremediation.

UNIT – V

Environmental Impact Assessment and Environmental Acts: Ecoplanning and

sustainable development: Indian standards IS: 2490, IS:3360, IS:3307, IS:2296, ISO: 14000

series, MINAS for industries and Ecomarks, Public liability insurance act, ElA guidelines and

assessment methods, Agenda 21 and Carbon credit.

References

1. Environmental Biotechnology by Alan Scragg. Pearson Education Limited, England.

2. Environmental biotechnology by S.N. Jogdand. Himalaya Publishing House.

Bombay.

3. Wastewater Engineering – Treatment, Disposal and Reuse. Metcalf and Eddy, Inc.,

Tata Mc Graw Hill, NewDelhi

4. Environmental chemistry by A.K. De Wiley Eastern Ltd. NewDelhi.

5. Introduction to Biodeterioration by D. Allsopp and k.J. Seal, ELBS/Edward

Arnold.

6. Environmental Science (5th Edition) by WP Cunninghum & BW Saigo., Mc Graw

Hill. 1999.

7. Biotechnology for Wastewater Treatment. P Nicholas Cheremisinoff. Prentice Hall

Of India. 2001

8. Biotechnological Methods of Pollution Control. SA Abbasi and E Ramaswami.

Universities Press.

9. Environmental Biotechnology, Concepts and Applications. Hans-Joachin Jordening

and JosefWinter. Winter-VCH. 2005

10. Biology of wastewater Treatment. N F Gray. Mc Graw Hill . 2004.

11. Environmental Biotechnology: Principles and Applications. Bruce Rittmann

and Perry McCarty, Mc Graw Hill

http://www.amazon.com/s/ref=ntt_athr_dp_sr_1?_encoding=UTF8&sort=relevancerank&search-alias=books&field-author=Bruce%20Rittmann

http://www.amazon.com/s/ref=ntt_athr_dp_sr_2?_encoding=UTF8&sort=relevancerank&search-alias=books&field-author=Perry%20McCarty


Page 21 of 33 SCAA Dt. 23.03.2011

Subject Title : Stem cell biology and Tissue Engineering

Course Number: 11BIOGE03 Number of credits: 4

Subject Decsription:

Scope: The course is to offer the student state of the art education of stem cells and how the

pluripotent and multipotent cells can be used to treat the neurodegenerative disorders,

cardiovascular disorders and diabetes. This course will also review the current scenario of

tissue engineering applications in bioartificial organs development and transplantation.

Objectives: The course will provide students with knowledge of wide ranging topics related

to stem cells, regenerative biology and tissue engineering.

Goal: The course goal is to introduce students to updated fundamental knowledge,

technological advancements and potential applications of stem cells and tissue engineering.

Unit-I

Introduction to Stem Cells – Definition, Classification, characteristics, Differentiation

and dedifferentiation, Stem cell niche, stem cell Vs cells; Basic culture procedures – Isolation,

culture methods, identification, stem cell markers, feeder layer; Instrumentations in stem cell

biology.

Unit-II

Different kinds of stem cells – Adult Stem cells, Embryonic stem cells, Embryonic Germ

cells, Heamtopoietic stem cell, Neural stem cells, muscle and cardiac stem cells, Umbilical cord

blood stem cells, cancer stem cells, Mesenchymal stem cells, Induced pluripotent Stem cells.

Unit-III

Therapeutic applications – stem cells and neurodegenerative disorders, stem cells and

diabetes, stem cells and cardiac disorders, regeneration of epidermis, Success stories of stem cell

therapy. Stem cell banking around the world. Current status of Stem cell research. World federal

fundings for stem cell research; Public view and ethical approaches on stem cells.

Unit – IV

Principles of Tissue Engineering – History and scope, Basics of Tissue Engineering,

Tissue Engineering triangle, Cell-ECM interaction, wound healing mechanism, Tissue

Engineering Bioreactors, Models of Tissue Engineering, Biomaterials in Tissue Engineering.

Unit – V

Bioartificial organs – source of cells, choosing the right scaffold material, mode of

transplantation. Epidermal Tissue engineering, Bladder reconstruction, Skin equivalents, Liver

reconstruction, Bone regeneration through tissue engineering, Tissue Engineering and future

perspectives.

Self study: Confocal Microscopy, Fluorescence microscopy, FACS.


Page 22 of 33 SCAA Dt. 23.03.2011

Reference

1. Stem cells: Scientific progress and future research directions – NIH report. Available @

www.stemcells.nih.gov/index ; www.stembook.org.

2. Essentials of Stem cell Biology – Robert Lanza, John Gearhart, Brigid Hogan.

3. Stem cell now – Christopher Thomas Scott.

4. Principles of Tissue Engineering – Robert Lanza.

5. Tissue Engineering – B.Palsson, J.A.Hubbell.

Subject Title : COMPUTATIONAL BIOLOGY



Scope: To provide molecular biologists the modern molecular databases and tools including

literature, sequence, structure and expression databases.

Objective: To provide information an understanding of the major computational problems in the

field of molecular biology.

Goal: To gain knowledge on molecular databases, comparative genomics, pattern search,

classification of sequence and structure, alignment of sequences, rapid similarity searching,

phylogenies, automated pattern learning, representing and searching protein structure, gene

expression profiling, clustering expressed genes, discovering transcription factor binding

sites,discovering common functions of co-expressed genes, metabolic pathways, signal

transduction pathways.

Contents:

Unit – I

Biological Data bases : Gen Bank: Sequence data / types; – Protein data bases-ESTs-

STSs – GSSs - HTGS; NCBI – PubMed – Entrez – BLAST – OMIM; Types of accession

numbers - Locus link, Uniigene, Entrez, EBI and Expasy.

Unit - II

Sequence Alignment: Alignment algorithms - Global and Local - Significance; BLAST

search steps - BLAST algorithm - BLAST search strategies; Advanced BLAST - Alignment

tools.

Unit - III

Gene Expression analysis tools: The mRNA- cDNA - Libraries ; Microarrrays:

Experimental design-Probe- Hybridization-Image analysis-Data analysis- Biological

confirmation - Microarray Databases.

http://www.stemcells.nih.gov/index

http://www.stembook.org/


Page 23 of 33 SCAA Dt. 23.03.2011

Unit - IV

Proteomic analysis tools: Protein domains and motifs - Bioinformatic tools for high

throughput protein analysis- protein structure- homology and functional genomics-

Unit V

Molecular Phylogeny and Genome analysis: Molecular evolution-Phylogenetic

analysis - Role of bioinformatics in taxonomy - Genome sequencing project - Genome

annotation –Bioinformatics perspective on human diseases.


Computational methods: Nucleic acid and protein sequence databases; data mining

methods for sequence analysis, web-based tools for sequence searches, motif analysis and

presentation.

References:

1. Bioinformatics and Functional Genomics by Pevsner, J. A John Wiley & Sons, Inc.,

USA.

2. Bioinformatics-A beginner’s guide by Jean – Michel Claverie and Cedric Notredame,

Wiley- Dream Tech India Pvt. Ltd.

3. Developing bioinformatics computer skills by Cynthia Gibas and Per Jambeck, O’

Reilly publications.

4. Introduction to bioinformatics by T.K. Attwood and D.J. Parry –Smith, Pearson

Education Asia.

5. Bioinformatics by David.W.Mount, CBS publishers and distributers.

6. Instant notes in bioinformatics by D.R. Westhead, J.H.Parish and R.M.Twyman.

7. Biostatistical analysis. Zar.J.H

8. Peuzner, P.A., Computational molecular Biology, An algorithmic approach.

Subject Title: Biosafety, Bioethics and IPR

Course Number: 1BIOBC11 Number of Credit Hours: 4(Four)

Subject Description:

Scope: This course has been designed to provide the student insights into these invaluable areas

of biotechnology, which play a crucial role in determining its future use and applications.

Objective: Students get an idea about the advantages and disadvantages of biotechnological

applications, ethical implications, and intellectual property rights.

Goal: To study the diversity of plants and animal life in a particular habitat, ethical issues

and potential of biotechnology for the benefit of man kind.

UNIT I

Introduction to biodiversity – levels of biodiversity –values of biodiversity – loss of

biodiversity – Species concept – Classification and systematics: biological nomenclature –

biological classification; Biodiversity conservation: in situ and ex situ - Magnitude and


Page 24 of 33 SCAA Dt. 23.03.2011

distribution of biodiversity - wild life biology – conservation strategies – measures of

biodiversity – biodiversity in India and global level – biodiversity hot spots.

UNIT II

Introduction to ethics/bioethics – Framework for ethical decision making; biotechnology

and ethics – biotechnology in agriculture and environment: benefits and risks – benefits and risks

of genetic engineering – ethical aspects of genetic testing – ethical aspects relating to use of

genetic information – genetic engineering and biowarfare.

UNIT III

Ethical implications of cloning: Reproductive cloning , therapeutic cloning ; Ethical,

legal and socio-economic aspects of gene therapy, germ line, somatic, embryonic and adult stem

cell research- GM crops and GMO’s – biotechnology and biopiracy – ELSI of human genome

project.

UNIT IV

Introduction to biosafety – biosafety issues in biotechnology – risk assessment and risk

management – safety protocols: risk groups – biosafety levels – biosafety guidelines and

regulations (National and International) – operation of biosafety guidelines and regulations –

types of biosafety containments.

UNIT V

Introduction to intellectual property and intellectual property rights – types: patents, copy

rights, trade marks, design rights, geographical indications – importance of IPR – patentable and

non patentables – patenting life – legal protection of biotechnological inventions – world

intellectual property rights organization (WIPO)

References:

1. Principles of cloning, Jose Cibelli, Robert P. lanza, Keith H. S . Campbell,

Michael D.West, Academic Press,2002Glimpses of Biodiversity – B.Bltosetti

2. Ehics in engineering, Martin. M.W. and Schinzinger.R. III Edition, Tata

McGraw-Hill, New Delhi. 2003.

3. http://books.cambridge.org/0521384737.htm

4. http://online.sfsu.edu/%7Erone/GEessays/gedanger.htm

5. http://www.actahort.org/members/showpdf?booknrarnr=447_125

6. http://www.cordis.lu/elsa/src/about.htm

7. http://www.biomedcentral.com/content/pdf/1472-6939-2-2.pdf

8. http://lifesciences.cornell.edu/vision/accelerating_focus05.php

9. http://thompson.com/libraries/fooddrug/

10. http://assets.cambridge.org/0521792495/sample/0521792495WS.PDF

11. http://europa.eu.int/eurlex/pri/en/oj/dat/1998/I_213/I_21319980730en00130021.pdf

12. http://www.clubofamsterdam.com/content.asp?contentid=281

13. Biosafety issues related to transgenic crops,DBT guidelines, Biotech Consortium

India Limited, New Delhi.


Page 25 of 33 SCAA Dt. 23.03.2011

Subject Title : Systems Biology


Subject description

Scope: Biology is fast becoming an interdisciplinary science. There is accumulation of large

amount of information in different areas of biology - on genome sequences of many organisms,

genetic and biochemical interaction networks, cell interactions during development, and

organism response to environmental stimuli, along with molecular understanding of diseases.

This has led to the emerging need for a holistic description of the working of biological systems

at different scales.

Objectives: Gain an appreciation for the field of systems biology. Understand and learn the

technical details of several current experiments or technologies used in the field of systems

biology. Understand some of the larger questions and issues with systems biology and large-

scale data collection and analysis.

Goal: This paper has been designed to give the students comprehensive training in the emerging

exciting upcoming area of Systems Biology, which will help students to get a career in both

industry/R&D.

UNIT-I

Systems Biology: Definition; Hypothesis driven research in systems biology: Wet

experiments – Dry experiments: predictions and simulations. Molecular databases: Accessibility,

compatibility, comprehensive database, portability, quality and navigability. Reductionist

approach and Integrative approach

UNIT-II

Genes and Genomes: Interpreting expression data using Gene Ontology; Evolution of

modularity and transcriptional networks, Riboswitches, metabolite sensing and translational

control- Microarrays – types and applications. Comparative genomics of non-coding sequence

UNIT-III

Pathway bioinformatics: Protein – carbohydrate metabolism – Biochemical cycles –

Interconnection of pathways – metabolic regulation – Translating biochemical networks into

linear algebra – KEGG: theory and practice.

UNIT-IV

OMICS Concepts: Genomics, Proteomics, Metabolomics, transcriptomics, intactomics,

Phenomics, localizomics; gene networks - Integration of Networks. Combination of omics

approaches: data integration, modeling and synthetic biology

UNIT-V

Computer Tools for Systems Biology: SimTK ; Gaggle; Systems Biology Workbench;

Systems Biology Markup Language; The CellML language; The little b Modeling Language;

Copasi (Version 4 of Gepasi); E-Cell System; StochSim; Virtual Cell; JigCell (John Tyson Lab);


Page 26 of 33 SCAA Dt. 23.03.2011

Python Simulator for Cellular Systems; Ingenuity Pathways Analysis; BIOREL; SAVI

Signaling Analysis and Visualization; JSim; BioNetGen; SBML-PET.

References:

1. Kitano H. Systems Biology: A Brief Overview. Science, 2002, 295: 1662-1664.

2. Ideker T. et al. A new approach to decoding life: Systems Biology. Annu. Rev. Genomics

Hum. Genet., 2001, 2: 343-372.

3. Ideker T. et al. Integrated Genomic and Proteomic Analyses of a Systematically

Perturbed Metabolic Network. Science, 2001, 292: 929-934

4. Ge H. et al. Integrating ‘omic’ information: a bridge between genomics and systems

biology. Trends in Genetics, 2003, 19, 10: 551-560.

5. Chong L et al., Whole-istic Biology, Science, Vol 295, no. 1, March 2002, p. 1661.

6. Catherine Brooksbank*, Graham Cameron and Janet Thornton. (2005).The European

Bioinformatics Institute’s data resources: towards systems biology. Nuc. AC Res.

33:D46-D53.

Subject Title : Pharmaceutical Biotechnology

Course Number : 11BIOBC13 Number of Credits:4 (Four)


Scope

This paper encodes information on drug designing, drug discovery and drug metabolism.

Objective

To enable the students to know the actual path of metabolism of drugs and drug discovery.

Goal

The information gained will help the students to formulate novel drugs.

UNIT I

Prokaryotic and Eukaryotic Cells in Biotech Production: Actinomycetes in Biotech

Production, Saccharomyces cerevisiae and Other Fungi in Biotech Production, Plants in Biotech

Production, Transgenic Plants as Functional Foods or Neutraceuticals Transgenic Plants and

Plant Cell Culture as Bioreactors of Secondary Metabolites, Transgenic Plants as Bioreactors of

Recombinant Protein.

UNIT II

Drug Modifications Pharmacodynamics of protein therapeutics; Chemical modification

of proteins/ therapeutics; Immuno suppressor in antibody therapy; Pharmaco

Genomics.,Molecular modification of lead compounds; Assay systems and models (e.g., Knock-

out Mice). Antisense technology as cell based therapeutics.


Page 27 of 33 SCAA Dt. 23.03.2011

UNIT III

Pharmaceuticals production in Plants: :Drugs derived from plants, , Antitumor agent -

Etoposide, Colchicine, Taxol, Vinblastine, Vincristine. Cardiotonic – Convallatoxin,

Acetyldigoxin, Adoniside, Antiinflammatory – Aescin, Bromelain, Choleretic – Curcumin,

Biopharmaceuticals Expressed in Plants Alternative Expression Systems, Three Promising

Examples: Tobacco (Rhizosecretion, Transfection) and Moss (Glycosylation)

UNIT IV

DNA Vaccines and antibody drug: DNA Vaccine Construction and Immunology

DNA Vaccine Expression Plasmids Delivery of DNA Vaccines. Peptide vaccine, Gene

Pharming, Cytokines as biopharmaceuticals, Rituximab, therapeutic enzymes.

UNIT V

Biogeneric Drugs Recombinant Therapeutic Proteins Erythropoietin (EPO), Colony-

stimulating Factors (CSFs), Human Growth Hormone (hGH), Insulins, Hepatitis B Vaccine,

Factor VIII (FVIII), Interferons (IFN) .Therapeutic hormone- insulin production through

recombinant DNA technology.

REFERENCE

1. Oliver Kayser, Rainer H. Müller, Wiley Publishers, 2005. Pharmaceutical Biotechnology:

Drug Discovery and Clinical Applications

2. Heinrich Klefenz, 2002, Industrial Pharmaceutical Biotechnology, WILEY-VCH Publication,

Germany.

3. Daan Crommelin, Robert D Sindelar, 2002, Pharmaceutical Biotechnology, Tailor and Francis

Publications, Newyork.

4. Jay P Rho, Stan G Louie, 2003, Hand book of Pharmaceutical Biotechnology, Pharmaceutical

products press, Newyork.

5. Lachman L Lieberman, HA, Kanig, J, 1986, Theory and practice of industrial pharmacy, 3rd

edition, Varghese publishing & Co, New Delhi.

6. 2000, Remington’s Pharamaceutial sciences, 18th

edtion, Mack publishing & Co., Easton,PA.


Page 28 of 33 SCAA Dt. 23.03.2011

Practicals - I : Basic Biotechnology

Subject code: 11BIOBCP1 Number of Credits:4 (Four)

Students are advised to collect the practical protocols well in advance from the respective

facult

Enzyme Biotechnology Laboratory - Dr. R. Boopathy

1. Determination of protein by Lowry method.

2. Determination of specific activity of the enzyme.

3. Determining the type of inhibitors for an enzyme.

4. Visualization of enzyme activity in Native PAGE.

Animal cell culture and Molecular Genetics Laboratory – Dr. V. Vijayapadma

5. Separation of peripheral mononuclear cells from the blood.

6. Culturing Lymphocytes from Peripheral blood samples.

7. Determination of Lipid peroxidation.

8. Assessing genotoxicity by COMET assay.

Molecular Toxicology Laboratory - Dr. P. Ekambaram

9. Hematology: RBC and WBC total counts, WBC differential count.

10. Mitotic index.

11. Micrometry.

12. Mounting of polytene chromosome from Chironomous larvae.

Plant Genetic Engineering Laboratory – Dr. R. Sathiskumar

12. Introduction to plant tissue culture-induction of callus and suspension cultures.

13. Isolation and purify the protoplasts and check its viability.

14. Induction of somatic embryogenesis and analysis of different stages.

15. Extract the genomic DNA from plants by CTAB method and resolve in the Agarose

Gel.

Plant Biotechnology Laboratory – Dr. S. Girija

16. Isolation of genomic DNA from medicinal plant by SDS method (Peterson et al.,

1993).

17. Staining of live plant cells.

18. Isolation of Ri plasmid from Agrobacterium rhizogenes.

19. Quantification of flavanoid content in fruit sample.

Molecular Microbiology Laboratory – Dr. S.R. Prabagaran

20. Isolation of Microorganisms from various environments (food, effluent, soil/sea,

Glaciers).

21. Cultivation of Bacteria, Actinomycetes, Fungi and Archaea.

22. Staining techniques and microscopy.

23. Biochemical observations of Bacteria (Antibiotics/Enzymes).


Page 29 of 33 SCAA Dt. 23.03.2011

Practicals – II : Advanced Biotechnology


Enzyme Biotechnology Laboratory – Dr. R. Boopathy

1. Identification of BChE gene using PCR.

2. Construction of BChE cDNA by reverse transcriptase.

3. Purification of BChE by DEAE cellulose column.

4. Determination of molecular weight of the protein by SDS PAGE.


5. Determination of antigen concentration by Radial immunodiffusion.

6. Determining antigen specificity by Double immunodiffusion.

7. Determination of antigen concentration by Rocket immunoelectrophoresis.

8. Passive heamagglutination assay for detection of soluble antigen.

Molecular Toxicology Laboratory – Dr. P. Ekambaram

9. Isolation of DNA from animal cells.

10. Estimation of Iron in water samples.

11. Estimation of chromium in water samples.

12. Drug administration methods.

Plant Genetic Engineering Laboratory – Dr. R. Sathishkumar

13. Particle gene gun mediated genetic transformation of GUS gene in tobacco.

14. Analysis of GUS gene in transgenic plants by histochemical staining

15. Identification of WT/ Transgenic plant by PCR.

16. Perform the restriction digestion for the given DNA sequence and comment.

Plant Biotechnology Laboratory – Dr. S. Girija

17. Micropropagation, callus induction and regeneration using different explants of

Plants.

18. Agrobacterium rhizogenes for hairy root culture.

19. Qualitative analysis of transgenic using phenolics content.

20. Estimation of Plumbagin (anticancer compound) in callus culture.

Molecular Microbiology Laboratory – Dr. S. R. Prabagaran

21. Mini prep of plasmid DNA and elution of DNA from gel.

22. Isolation of RNA from bacteria.

23. Competent cell and Electrocompetent cell preparation.

24. Transformation and Electroporation.


Page 30 of 33 SCAA Dt. 23.03.2011

Practicals – III : Applied Biotechnology


Enzyme Biotechnology Laboratory – Dr. R. Boopathy

1. Prediction and validation of protein structure (AChE using modellar)

2. Prediction of binding mode of receptor ligand (AChE/Tacrine/Gallanthamine)

3. Determination of interactive residues on ligand receptor complexes

(chimera/SPV/PyMol).

4. Sequence analysis of nucleic acid (BLAST, MSV), motif analysis and domain

identification for protein.


5. Checking the cell viability by MTT assay

6. Determination of cytotoxicity by Nitric oxide assay

7. Determination of cytotoxicity by measuring lactate dehydrogenase activity

8. Determination of Apoptosis through DNA fragmentation analysis

Molecular Toxicology Laboratory - Dr. P. Ekambaram

9. Preparation of primary cells from chick embryo.

10. Cell counting and cell viability.

11. Trypsinization of monolayer and subculturing

12. Sex chromatin identification from Buccal smear

Plant Genetic Engineering Laboratory – Dr. R. Sathishkumar

13. Screening of rice germplasm for aroma using PCR-RFLP analysis

14. Transient gene expression in tobacco by infiltration of Agrobacterium culture

15. Determination of protein expression (transgene) by western blotting

16. Pair wise and multiple sequence alignment of nucleic acids and proteins

Plant Biotechnology Laboratory - Dr. S. Girija

17. Determination of Free radical scavenging activity by DPPH assay

18. Determination of secondary metabolite (Eugenol) using TLC and confirmation by HPLC

19. Determination of Iron chelating activity of medicinal plant extract

20. ISSR marker analysis for medicinal plant identification.

Molecular Microbiology Laboratory - Dr. S.R. Prabagaran

21. Metagenomic DNA isolation from problem soils

22. Estimation of mol% G+C content of DNA (Tm)

23. Detection of FAMEs through GAS chromatography

24. Southern blotting/dot blotting


Page 31 of 33 SCAA Dt. 23.03.2011

Course: Supportive I –Tools in Biotechnology

Subject Code: 11BIOGS01 Number of Credits:2 (Two)

UNIT-I:

Gene and Genomes

Prokaryotic and Eukaryotic Genomes - Structure of Gene - DNA as the genetic material; Extra

chromosomal DNA: Plasmid, mitochondrial DNA and chloroplast DNA.

UNIT-II:

Cloning Vectors

Vectors: Plasmid, phagemid, cosmid, Artificial Chromosomes (BAC) - Transformation

techniques: Electroporation, CaCl2 method.

UNIT-III:

Tools for Gene Manipulation

Enzymes: Gel Electrophoresis: AGE and PAGE; Restriction Enzymes, Ligases, Modifying

Enzymes - Markers for Selection: selectable and scorable - Examples.

UNIT-IV:

Selection Strategy and Screening for Transformants

Selection of rDNA Clones: Blue-White Selection, Colony Hybridization, PCR, Molecular

analysis: Western blotting, Southern Blotting and Northern Blotting.

UNIT-V:

Application of Cloning

Over expression of Biomolecules (Insulin) - Gene therapy – GMO – DNA Finger printing

Application and Biosafety issues

References

1. Primrose. S.B., Twyman R.M., Old. R.W. (2001) Principles of Gene Manipulation.

Blackwell Science Limited.

2. Molecular Biotechnology. S.B Primrose, Blackwell Scientific Publishers, Oxford,

1994.

3. Principles of Gene Manipulation. T.A.Brown

4. DNA Science – A first course in rDNA technology, D.A. Mickloss nd G.A.Freyar, Cold

Spring Harbor laboratory Press, New York, 1990.

5. Molecular Cloning. Maniatis, Fritsch and Sambrook.a


Page 32 of 33 SCAA Dt. 23.03.2011

Course: Supportive II- Medical Biotechnology

Subject Code: 11BIOGS02 Number of Credits:2 (Two)

Unit I

Introduction to Biotechnology and medicine:

Medicine field of 21st century, Role of Biotechnology in medicine, rDNA technology, Vaccines,

MoABS.

Unit II

Molecular Diagnostics:

Importans of diagnosis-PCR based diagnosis for infections diseases (HIV, Hepatitis, Typoid,

Filariasis) ,Cancer and genetic disorders

Unit III

Cell and gene mediated therapy:

Introdcution to stem cells-History ofstem cell research-Classification of stem cells –Stem cell

banking-applications of stem cells-importance of stemcells- regulations of stem cell research -

Gene theraoy;outline and methods.

Unit IV

Assisted reproductive techniques:

Introdcution-causes of infertility-methods;IVF-Intra uterine insemination-cryopreservaton of

germcells.

Unit V

Tissue Engineering

Introduction-Bioartificial organs-Historical backgrogund-liver-kidney-skin-pancreas-Urinary

bladder-bone-Challenges and advantages.

Ref: Medical Biotechnology-P.C.Trivedi(2008)


Page 33 of 33 SCAA Dt. 23.03.2011

Course: Supportive III - PLANT MOLECULAR FARMING

Subject Code: 11BIOGS03 Number of Credits: 2 (Two)

Unit I

Production technologies

Efficient and reliable production of pharmaceuticals in alfalfa; Foreign protein expression

using plant cell suspension and cultures; Novel sprouting technology for recombinal protein

production monocot expression systems for molecular farming the field evaluation of transgenic

crops engineered to produce recombinant proteins; plant viral vectors: history and new

developments

Unit II

Pharmaceuticals

Production of pharmaceutical proteins in plants and plant cell suspension cultures;

chloroplast derived antibodies, biopharmaceuticals and edible vaccines; plant-derived vaccines:

progress and constraints; production of secretory IgA in transgenic plants

Unit II

Field trial

Production of spider silk proteins in transgenic tobacco and potato ;Gene farming in pea

under field conditions

Unit-IV

Production

Host plants, systems ad expression strategies for molecular farming; Downstream

processing of plant-derived recombinant therapeutic proteins; Glycosylation of plant-made

pharmaceuticals

Unit-V

Product issues

Biosafety aspects of molecular farming in plants; A top-down view of molecular farming

from the pharmaceutical industry: requirements and expectations; The role of science and

discourse in the application of the precautionary approach

Reference:

1. Molecular farming:Plant made pharmaceuticals and technical proteins (2004) Eds.Rainer

Fischer and Stefan schillberg , Wiley publishers,USA

Documents

BHARATHIAR UNIVERSITY COIMBATORE – 641 046syllabus.b-u.ac.in/unidepts/1112/biotech1112.pdf · BHARATHIAR UNIVERSITY :: COIMBATORE – 641 046 ... Origin and evolution of microorganisms